Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA296506 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The binding specificity and regulatory effect of WT and redesigned Puf2p [RNA-Seq]
| PRJNA296423 | ENA
Project description:PUF proteins have become a leading scaffold for designing RNA-binding proteins to contact and control RNAs at will. We analyze the effects of that reengineering across the transcriptome in vivo for the first time. We show, by HITS-CLIP and PAR-CLIP, that S. cerevisiae Puf2p, a non-canonical PUF protein, binds more than 1000 mRNA targets. Puf2p binds multiple UAAU elements, unlike canonical PUF proteins. We also perform CLIP-seq on truncations of Puf2p, showing that its prion domain is dispensable for WT binding. We design a modified Puf2p to bind UAAG rather than UAAU, which allows us to align the protein with the binding site. In vivo, the redesigned protein binds UAAG sites. Its altered specificity redistributes the protein away from 3âUTRs, such that the protein tracks with its sites and binds throughout the mRNA. We use RNA-seq to determine that R1 SNE Puf2p represses a novel RNA network. CLIP-seq was performed in BY4742 S. cerevisiae grown in log phase, and using 2 replicates of TAP-tagged proteins. RNA-seq was performed to determine the regulatory effect of WT or mutant Puf2p, using 4 replicates of the control (no Puf2p), 3 of WT Puf2p and 4 of R1 SNE Puf2p.
2015-12-15 | E-GEOD-73227 | biostudies-arrayexpress
Project description:Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
| PRJNA151519 | ENA
Project description:Protein-RNA interactions are integral components of nearly every aspect of biology including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. Here, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTR) covering 72% of protein-coding transcripts encoded in the genome, confirming 3M-bM-^@M-^Y UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3M-bM-^@M-^Y UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression. Our study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo. Duplicate gPAR-CLIP and mRNA-seq libraries were sequenced from yeast strains for each of three conditions: log-phase growth, growth after 2 hour glucose starvation, and growth after 2 hour nitrogen starvation. Additional duplicate mRNA-seq libraries were sequenced from yeast strains grown in the absence of 4-thiouracil. gPAR-CLIP libraries were used to determine regions of mRNA bound by proteins. mRNA-seq libraries served as controls for mRNA abundance. A Puf3p PAR-CLIP library was sequenced to determine how well gPAR-CLIP captured the binding signatures of a single RNA-binding protein.
2013-01-29 | E-GEOD-43747 | biostudies-arrayexpress
Project description:DIP-chip: Rapid and accurate determination of DNA-binding specificity
| PRJNA97819 | ENA
Project description:High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors
| PRJNA110437 | ENA
Project description:A TATA binding protein regulatory network
| PRJNA97865 | ENA
Project description:MNase-seq Experiments from Calorie Restricted and Non-Restricted Yeast from WT, ISW2DEL and ISW2K215R strains
2014-09-15 | GSE53718 | GEO
Project description:Nuclear depletion of the essential transcription termination factor Nrd1 in Saccharomyces cerevisiae was studied using a combination of RNA-Seq, ChIP-Seq of Pol II and PAR-CLIP of Nrd1. The drug rapamycin induces the formation of a ternary complex between a protein of interest, the drug and the small subunit of the ribosome (both proteins are genetically engineered). The small ribosome subunit is transported out of the nucleus. therefore the protein of interest can be depleted from nucleus upon treatment with rapamycin.
2013-11-14 | E-MTAB-1766 | biostudies-arrayexpress
Project description:PUF proteins have become a leading scaffold for designing RNA-binding proteins to contact and control RNAs at will. We analyze the effects of that reengineering across the transcriptome in vivo for the first time. We show, by HITS-CLIP and PAR-CLIP, that S. cerevisiae Puf2p, a non-canonical PUF protein, binds more than 1000 mRNA targets. Puf2p binds multiple UAAU elements, unlike canonical PUF proteins. We also perform CLIP-seq on truncations of the Puf2p, showing that its prion domain is dispensable for WT binding. We design a modified Puf2p to bind UAAG rather than UAAU, which allows us to align the protein with the binding site. In vivo, the redesigned protein binds UAAG sites. Its altered specificity redistributes the protein away from 3âUTRs, such that the protein tracks with its sites, binds throughout the mRNA. We use RNA-seq to determine that R1 SNE Puf2p represses a novel RNA network. CLIP-seq was performed in BY4742 S. cerevisiae grown in log phase, and using 2 replicates of TAP-tagged proteins.
2015-12-15 | E-GEOD-73273 | biostudies-arrayexpress